An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• RNA degradation is crucial for bacterial gene regulation and adaptation.
• Endoribonucleases (endoRNases) initiate degradation, followed by exoribonucleases (exoRNases).
• Genome-wide studies on the coordinated action of these enzymes are limited.

Purpose of the Study:

• To investigate the coordinated action between endoRNase Y and 3'-to-5' exoRNases (PNPase, YhaM, RNase R) in Streptococcus pyogenes.
• To identify the RNA targets and processing events mediated by these enzymes.
• To understand the interplay between endo- and exoRNases in bacterial RNA metabolism.

Main Methods:

• Comparative analysis of endoRNase Y targetome with 3'-to-5' exoRNase targetomes.
• Identification of RNA cleavage sites and processing patterns.
• Development of a strategy to detect processing events and enzyme interplay.

Main Results:

• EndoRNase Y preferentially cleaves RNA after guanosine residues.
• RNase Y generates RNA substrates subsequently trimmed at the 3' end by PNPase and YhaM.
• RNase Y-generated 5' ends are generally not further processed by these exoRNases.
• The study identified previously undetectable processing events.

Conclusions:

• EndoRNase Y plays a key role in initiating RNA degradation by generating substrates for specific exoRNases.
• PNPase and YhaM actively process RNA fragments generated by RNase Y.
• This research provides a genome-wide perspective on the interplay between bacterial endo- and exoRNases.